Suggestion: Make waterproof pipes compatible with the water mill.

Already a mod out there that does both.

Short answer: NO.

Long Answer: Still NO. It has been discussed before, and alblaka said that he doesn't want manned water mills to work like that. (Its a link)

Quote from asmodous

Will go look around for the mod that does that though as I feel the cost of the pump + pipes ways out the energy you get from it. Thanks.

Fact it doesn't. you are failing to notice that water source blocks are pretty easy to duplicate to the point it becomes basically infinite.

Making water mills compatible with waterproof pipes would let one build a pump over an infinite water source going to the mill for a massive EU gain over unmanned mills, so no.

Or it should produce less EU(per units of water, but more max input, because of what I will say), thinking to the cost of the pump. Should generate a little bit more (arround 20%) that Generator with pump running with Steam Engine.
So with redstone engine, it would be a very little amount of EU.
(I think less than what you produce when water source are surrounding your Watermill, no ? I don't know the ratio Redstone Engine Power/Steam Engine Power but I think it's very low.

PS: we can already use BC) in order to use Water Bucket in the upper slot and produce 2 EU/tick, without any Coal cost.